Variant report

Variant	rs10459588
Chromosome Location	chr15:44365946-44365947
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 139 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:130)

rs_ID	r²[population]
rs10518994	1.00[CEU][hapmap];0.90[AMR][1000 genomes]
rs10851415	1.00[CEU][hapmap]
rs10851416	1.00[CEU][hapmap]
rs11070419	1.00[CEU][hapmap]
rs1115870	1.00[CEU][hapmap]
rs1160066	1.00[CEU][hapmap];0.81[AMR][1000 genomes]
rs11631340	1.00[CEU][hapmap];0.90[AMR][1000 genomes]
rs11635948	1.00[CEU][hapmap];1.00[JPT][hapmap];0.80[YRI][hapmap];0.93[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs11854312	1.00[CEU][hapmap];0.90[AMR][1000 genomes]
rs11857696	1.00[CEU][hapmap];0.87[AMR][1000 genomes]
rs12324261	1.00[CEU][hapmap]
rs12437804	1.00[CEU][hapmap];0.90[AMR][1000 genomes]
rs12591537	1.00[CEU][hapmap];0.90[AMR][1000 genomes]
rs12900237	1.00[CEU][hapmap]
rs12900880	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.97[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs12910886	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs1426657	1.00[CEU][hapmap]
rs1426658	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.97[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs16952932	1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs16958670	1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs16958691	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs1808509	1.00[CEU][hapmap];0.81[AMR][1000 genomes]
rs1820482	1.00[CEU][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.97[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs1834641	1.00[CEU][hapmap]
rs2015277	1.00[CEU][hapmap]
rs2019074	0.81[AMR][1000 genomes]
rs2042738	1.00[CEU][hapmap]
rs2042739	1.00[CEU][hapmap]
rs2042741	1.00[CEU][hapmap];0.87[AMR][1000 genomes]
rs2114420	0.90[AMR][1000 genomes]
rs2114421	1.00[CEU][hapmap];0.90[AMR][1000 genomes]
rs2114422	1.00[CEU][hapmap]
rs2162366	1.00[CEU][hapmap]
rs2217108	1.00[CEU][hapmap]
rs2252959	1.00[ASN][1000 genomes]
rs2412845	1.00[CEU][hapmap]
rs2412846	1.00[CEU][hapmap]
rs2412849	1.00[CEU][hapmap]
rs2412850	1.00[CEU][hapmap];0.90[AMR][1000 genomes]
rs2412851	1.00[CEU][hapmap]
rs2412852	0.90[AMR][1000 genomes]
rs2412854	1.00[CEU][hapmap]
rs2412855	0.90[AMR][1000 genomes]
rs2555375	1.00[CEU][hapmap]
rs2555376	1.00[CEU][hapmap]
rs2555380	1.00[CEU][hapmap]
rs2555384	1.00[CEU][hapmap]
rs2555387	1.00[CEU][hapmap]
rs2555389	1.00[CEU][hapmap]
rs2615278	1.00[CEU][hapmap]
rs2615279	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs2615281	1.00[CEU][hapmap]
rs2615285	1.00[CEU][hapmap]
rs2615287	1.00[CEU][hapmap]
rs2615288	1.00[CEU][hapmap]
rs2615293	1.00[CEU][hapmap]
rs2615294	1.00[CEU][hapmap]
rs2615295	1.00[CEU][hapmap];0.81[AMR][1000 genomes]
rs2615297	1.00[CEU][hapmap]
rs2615299	1.00[CEU][hapmap]
rs2623019	1.00[CEU][hapmap];0.87[AMR][1000 genomes]
rs2696085	0.91[ASN][1000 genomes]
rs2696086	0.91[ASN][1000 genomes]
rs2696088	0.91[ASN][1000 genomes]
rs2696091	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs2696094	1.00[CEU][hapmap]
rs2696098	1.00[CEU][hapmap]
rs2706472	1.00[CEU][hapmap]
rs2706473	1.00[CEU][hapmap]
rs2706474	0.81[AMR][1000 genomes]
rs2706481	1.00[CEU][hapmap];0.87[AMR][1000 genomes]
rs2706486	1.00[CEU][hapmap]
rs2706487	1.00[CEU][hapmap]
rs2706488	1.00[CEU][hapmap];0.87[AMR][1000 genomes]
rs2706490	1.00[CEU][hapmap]
rs2706495	1.00[CEU][hapmap]
rs2733203	1.00[CEU][hapmap]
rs2733204	1.00[CEU][hapmap]
rs2733208	1.00[CEU][hapmap]
rs2733209	1.00[CEU][hapmap]
rs2733213	1.00[CEU][hapmap]
rs2733221	1.00[CEU][hapmap]
rs2733226	1.00[CEU][hapmap];0.87[AMR][1000 genomes]
rs28479591	1.00[ASN][1000 genomes]
rs28656778	1.00[ASN][1000 genomes]
rs28832708	1.00[ASN][1000 genomes]
rs2899103	1.00[CEU][hapmap]
rs2929281	1.00[CEU][hapmap]
rs2929282	1.00[JPT][hapmap]
rs2930528	1.00[CEU][hapmap]
rs2950619	1.00[ASN][1000 genomes]
rs2950620	0.91[ASN][1000 genomes]
rs2952447	0.91[ASN][1000 genomes]
rs2957581	1.00[CEU][hapmap];0.81[AMR][1000 genomes]
rs2957583	1.00[CEU][hapmap];0.90[AMR][1000 genomes]
rs4419034	1.00[CEU][hapmap];0.90[AMR][1000 genomes]
rs4923976	1.00[CEU][hapmap]
rs4924727	1.00[CEU][hapmap];0.90[AMR][1000 genomes]
rs4924728	1.00[CEU][hapmap];1.00[JPT][hapmap];0.80[YRI][hapmap];0.93[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs4924729	1.00[CEU][hapmap]
rs4924734	1.00[CEU][hapmap]
rs4924737	1.00[CEU][hapmap]
rs57575746	0.96[ASN][1000 genomes]
rs58008065	1.00[ASN][1000 genomes]
rs58278421	0.83[ASN][1000 genomes]
rs58541819	0.83[ASN][1000 genomes]
rs58882193	1.00[ASN][1000 genomes]
rs60536495	0.88[ASN][1000 genomes]
rs6493092	1.00[CEU][hapmap]
rs6493093	1.00[CEU][hapmap]
rs6493094	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.97[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs6493096	1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs6493098	1.00[ASN][1000 genomes]
rs7162529	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs7166715	1.00[CEU][hapmap]
rs7179696	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs8029187	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs8029425	1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs8033233	1.00[CEU][hapmap]
rs8035212	1.00[CEU][hapmap];0.90[AMR][1000 genomes]
rs8035382	1.00[JPT][hapmap]
rs8035402	1.00[JPT][hapmap]
rs8036541	1.00[CEU][hapmap]
rs8037596	1.00[CEU][hapmap]
rs8038096	1.00[CEU][hapmap];0.87[AMR][1000 genomes]
rs8041328	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs8041487	1.00[CEU][hapmap]
rs890465	1.00[CEU][hapmap];0.90[AMR][1000 genomes]
rs958485	1.00[CEU][hapmap];0.90[AMR][1000 genomes]
rs9920249	1.00[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv431387	chr15:43929378-44862930	Weak transcription Strong transcription Active TSS ZNF genes & repeats Enhancers Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	158 gene(s)	inside rSNPs	diseases
2	nsv931051	chr15:43988761-44833518	Strong transcription Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	154 gene(s)	inside rSNPs	diseases
3	nsv1044435	chr15:44176103-44507403	Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases
4	nsv1052511	chr15:44266441-44719023	Flanking Active TSS Enhancers Weak transcription Strong transcription Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	29 gene(s)	inside rSNPs	diseases
5	nsv542371	chr15:44266441-44719023	Flanking Active TSS Enhancers Weak transcription Active TSS Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	29 gene(s)	inside rSNPs	diseases
6	nsv1045362	chr15:44280481-44414443	Enhancers Weak transcription ZNF genes & repeats Bivalent Enhancer Flanking Active TSS Active TSS Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	n/a
7	nsv832989	chr15:44306469-44461710	Enhancers Genic enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
8	esv3351630	chr15:44334624-44547841	Weak transcription Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
9	esv3331124	chr15:44340909-44367883	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription	TF binding region Chromatin interactive region	1 gene(s)	inside rSNPs	n/a

No data

Chromatin state (count:9 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:44359200-44366800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr15:44359200-44373000	Weak transcription	NH-A	brain
3	chr15:44362000-44366800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
4	chr15:44363400-44373200	Weak transcription	Brain Cingulate Gyrus	brain
5	chr15:44363600-44367000	Weak transcription	Brain Hippocampus Middle	brain
6	chr15:44363800-44367000	Weak transcription	Brain Substantia Nigra	brain
7	chr15:44365600-44367800	Enhancers	NHEK	skin
8	chr15:44365800-44366000	Enhancers	Breast Myoepithelial Primary Cells	Breast
9	chr15:44365800-44367800	Enhancers	HMEC	breast

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